Provided by: globus-gram-job-manager-doc_13.53-1_all 
NAME
globus_gram_job_manager_interface_tutorial - GRAM Job Manager Scheduler Tutorial This
tutorial describes the steps needed to build a GRAM Job Manager Scheduler interface
package.
The audience for this tutorial is a person interested in adding support for a new
scheduler interface to GRAM. This tutorial will assume some familiarty with GTP, autoconf,
automake, and Perl. As a reference point, this tutorial will refer to the code in the LSF
Job Manager package.
Writing a Scheduler Interface
This section deals with writing the perl module which implements the interface between the
GRAM job manager and the local scheduler. Consult the Job Manager Scheduler Interface
section of this manual for a more detailed reference on the Perl modules which are used
here.
The scheduler interface is implemented as a Perl module which is a subclass of the
Globus::GRAM::JobManager module. Its name must match the scheduler type string used when
the service is installed. For the LSF scheduler, the name is lsf, so the module name is
Globus::GRAM::JobManager::lsf and it is stored in the file lsf.pm. Though there are
several methods in the JobManager interface, they only ones which absolutely need to be
implemented in a scheduler module are submit, poll, cancel.
We'll begin by looking at the start of the lsf source module, lsf.in (the transformation
to lsf.pm happens when the setup script is run. To begin the script, we import the GRAM
support modules into the scheduler module's namespace, declare the module's namespace, and
declare this module as a subclass of the Globus::GRAM::JobManager module. All scheduler
packages will need to do this, substituting the name of the scheduler type being
implemented where we see lsf below.
use Globus::GRAM::Error;
use Globus::GRAM::JobState;
use Globus::GRAM::JobManager;
use Globus::Core::Paths;
...
package Globus::GRAM::JobManager::lsf;
@ISA = qw(Globus::GRAM::JobManager);
Next, we declare any system-specifc values which will be substituted when the setup
package scripts are run. In the LSF case, we need the know the paths to a few programs
which interact with the scheduler:
my ($mpirun, $bsub, $bjobs, $bkill);
BEGIN
{
$mpirun = '@MPIRUN@';
$bsub = '@BSUB@';
$bjobs = '@BJOBS@';
$bkill = '@BKILL@';
}
The values surrounded by the at-sign (such as @MPIRUN@) will be replaced by with the path
to the named programs by the find-lsf-tools script described below.
Writing a constructor
For scheduler interfaces which need to setup some data before calling their other methods,
they can overload the new method which acts as a constructor. Scheduler scripts which
don't need any per-instance initialization will not need to provide a constructor, the
Globus::GRAM::JobManager constructor will do the job.
If you do need to overloaded this method, be sure to call the JobManager module's
constructor to allow it to do its initialization, as in this example:
sub new
{
my $proto = shift;
my $class = ref($proto) || $proto;
my $self = $class->SUPER::new(@_);
## Insert scheduler-specific startup code here
return $self;
}
The job interface methods are called with only one argument, the scheduler object itself.
That object contains the a Globus::GRAM::JobDescription object ($self->{JobDescription})
which includes the values from the RSL string associated with the request, as well as a
few extra values:
job_id
The string returned as the value of JOB_ID in the return hash from submit. This won't
be present for methods called before the job is submitted.
uniq_id
A string associated with this job request by the job manager program. It will be
unique for all jobs on a host for all time.
cache_tag
The GASS cache tag related to this job submission. Files in the cache with this tag
will be cleaned by the cleanup_cache() method.
Now, let's look at the methods which will interface to the scheduler.
Submitting Jobs
All scheduler modules must implement the submit method. This method is called when the job
manager wishes to submit the job to the scheduler. The information in the original job
request RSL string is available to the scheduler interface through the JobDescription data
member of it's hash.
For most schedulers, this is the longest method to be implemented, as it must decide what
to do with the job description, and convert them to something which the scheduler can
understand.
We'll look at some of the steps in the LSF manager code to see how the scheduler interface
is implemented.
In the beginning of the submit method, we'll get our parameters and look up the job
description in the manager-specific object:
sub submit
{
my $self = shift;
my $description = $self->{JobDescription};
Then we will check for values of the job parameters that we will be handling. For example,
this is how we check for a valid job type in the LSF scheduler interface:
if(defined($description->jobtype())
{
if($description->jobtype !~ /^(mpi|single|multiple)$/)
{
return Globus::GRAM::Error::JOBTYPE_NOT_SUPPORTED;
}
elsif($description->jobtype() eq 'mpi' && $mpirun eq "no")
{
return Globus::GRAM::Error::JOBTYPE_NOT_SUPPORTED;
}
}
The lsf module supports most of the core RSL attributes, so it does more processing to
determine what to do with the values in the job description.
Once we've inspected the JobDescription we'll know what we need to tell the scheduler
about so that it'll start the job properly. For LSF, we will construct a job description
script and pass that to the bsub command. This script is a bourne shell script with some
special comments which LSF uses to decide what constraints to use when scheduling the job.
First, we'll open the new file, and write the file header:
$lsf_job_script = new IO::File($lsf_job_script_name, '>');
$lsf_job_script->print<<EOF;
#! /bin/sh
#
# LSF batch job script built by Globus Job Manager
#
EOF
Then, we'll add some special comments to pass job constraints to LSF:
if(defined($queue))
{
$lsf_job_script->print("#BSUB -q $queue0);
}
if(defined($description->project()))
{
$lsf_job_script->print("#BSUB -P " . $description->project() . "0);
}
Before we start the executable in the LSF job description script, we will quote and escape
the job's arguments so that they will be passed to the application as they were in the job
submission RSL string:
At the end of the job description script, we actually run the executable named in the
JobDescription. For LSF, we support a few different job types which require different
startup commands. Here, we will quote and escape the strings in the argument list so that
the values of the arguments will be identical to those in the initial job request string.
For this Bourne-shell syntax script, we will double-quote each argument, and escaping the
backslash (), dollar-sign ($), double-quote ("), and single-quote (') characters. We will
use this new string later in the script.
@arguments = $description->arguments();
foreach(@arguments)
{
if(ref($_))
{
return Globus::GRAM::Error::RSL_ARGUMENTS;
}
}
if($arguments[0])
{
foreach(@arguments)
{
$_ =~ s/\/\\/g;
$_ =~ s/\g;
$_ =~ s/"/\
$_ =~ s/`/\`/g;
$args .= '"' . $_ . '" ';
}
}
else
{
$args = "";
}
To end the LSF job description script, we will write the command line of the executable to
the script. Depending on the job type of this submission, we will need to start either one
or more instances of the executable, or the mpirun program which will start the job with
the executable count in the JobDescription:
if($description->jobtype() eq "mpi")
{
$lsf_job_script->print("$mpirun -np " . $description->count() . " ");
$lsf_job_script->print($description->executable()
. " $args 0);
}
elsif($description->jobtype() eq 'multiple')
{
for(my $i = 0; $i < $description->count(); $i++)
{
$lsf_job_script->print($description->executable() . " $args &0);
}
$lsf_job_script->print("wait0);
}
else
{
$lsf_job_script->print($description->executable() . " $args0);
}
Next, we submit the job to the scheduler. Be sure to close the script file before trying
to redirect it into the submit command, or some of the script file may be buffered and
things will fail in strange ways!
When the submission command returns, we check its output for the scheduler-specific job
identifier. We will use this value to be able to poll or cancel the job.
The return value of the script should be either a GRAM error object or a reference to a
hash of values. The Globus::GRAM::JobManager documentation lists the valid keys to that
hash. For the submit method, we'll return the job identifier as the value of JOB_ID in the
hash. If the scheduler returned a job status result, we could return that as well. LSF
does not, so we'll just check for the job ID and return it, or if the job fails, we'll
return an error object:
$lsf_job_script->close();
$job_id = (grep(/is submitted/,
split(/0, `$bsub < $lsf_job_script_name`)))[0];
if($? == 0)
{
$job_id =~ m/<([^>]*)>/;
$job_id = $1;
return { JOB_ID => $job_id };
}
return Globus::GRAM::Error::INVALID_SCRIPT_REPLY;
}
That finishes the submit method. Most of the functionality for the scheduler interface is
now written. We just have a few more (much shorter) methods to implement.
Polling Jobs
All scheduler modules must also implement the poll method. The purpose of this method is
to check for updates of a job's status, for example, to see if a job has finished.
When this method is called, we'll get the job ID (which we returned from the submit method
above) as well as the original job request information in the object's JobDescription. In
the LSF script, we'll pass the job ID to the bjobs program, and that will return the job's
status information. We'll compare the status field from the bjobs output to see what job
state we should return.
If the job fails, and there is a way to determine that from the scheduler, then the script
should return in its hash both
JOB_STATE => Globus::GRAM::JobState::FAILED
and
ERROR => Globus::GRAM::Error::<ERROR_TYPE>->value
Here's an excerpt from the LSF scheduler module implementation:
sub poll
{
my $self = shift;
my $description = $self->{JobDescription};
my $job_id = $description->jobid();
my $state;
my $status_line;
$self->log("polling job $job_id");
# Get first line matching job id
$_ = (grep(/$job_id/, `$bjobs $job_id 2>/dev/null`))[0];
# Get 3th field (status)
$_ = (split(/))[2];
if(/PEND/)
{
$state = Globus::GRAM::JobState::PENDING;
}
elsif(/USUSP|SSUSP|PSUSP/)
{
$state = Globus::GRAM::JobState::SUSPENDED
}
...
return {JOB_STATE => $state};
}
Cancelling Jobs
All scheduler modules must also implement the cancel method. The purpose of this method is
to cancel a running job.
As with the poll method described above, this method will be given the job ID as part of
the JobDescription object held by the manager object. If the scheduler interface provides
feedback that the job was cancelled successfully, then we can return a JOB_STATE change to
the FAILED state. Otherwise we can return an empty hash reference, and let the poll method
return the state change next time it is called.
To process a cancel in the LSF case, we will run the bkill command with the job ID.
sub cancel
{
my $self = shift;
my $description = $self->{JobDescription};
my $job_id = $description->jobid();
$self->log("cancel job $job_id");
system("$bkill $job_id >/dev/null 2>/dev/null");
if($? == 0)
{
return { JOB_STATE => Globus::GRAM::JobState::FAILED }
}
return Globus::GRAM::Error::JOB_CANCEL_FAILED;
}
End of the script
It is required that all perl modules return a non-zero value when they are parsed. To do
this, make sure the last line of your module consists of:
1;
Setting up a Scheduler
Once we've written the job manager script, we need to get it installed so that the
gatekeeper will be able to run our new service. We do this by writing a setup script. For
LSF, we will write the script setup-globus-job-manager-lsf.pl, which we will list in the
LSF package as the Post_Install_Program.
To set up the Gatekeeper service, our LSF setup script does the following:
1. Perform system-specific configuration.
2. Install the GRAM scheduler Perl module and register as a gatekeeper service.
3. (Optional) Install an RSL validation file defining extra scheduler-specific RSL
attributes which the scheduler interface will support.
4. Update the GPT metadata to indicate that the job manager service has been set up.
System-Specific Configuration
First, our scheduler setup script probes for any system-specific information needed to
interface with the local scheduler. For example, the LSF scheduler uses the mpirun, bsub,
bqueues, bjobs, and bkill commands to submit, poll, and cancel jobs. We'll assume that the
administrator who is installing the package has these commands in their path. We'll use an
autoconf script to locate the executable paths for these commands and substitute them into
our scheduler Perl module. In the LSF package, we have the find-lsf-tools script, which is
generated during bootstrap by autoconf from the find-lsf-tools.in file:
## Required Prolog
AC_REVISION($Revision: 1.7 $)
AC_INIT(lsf.in)
# checking for the GLOBUS_LOCATION
if test "x$GLOBUS_LOCATION" = "x"; then
echo "ERROR Please specify GLOBUS_LOCATION" >&2
exit 1
fi
...
## Check for optional tools, warn if not found
AC_PATH_PROG(MPIRUN, mpirun, no)
if test "$MPIRUN" = "no" ; then
AC_MSG_WARN([Cannot locate mpirun])
fi
...
## Check for required tools, error if not found
AC_PATH_PROG(BSUB, bsub, no)
if test "$BSUB" = "no" ; then
AC_MSG_ERROR([Cannot locate bsub])
fi
...
## Required epilog - update scheduler specific module
prefix='$(GLOBUS_LOCATION)'
exec_prefix='$(GLOBUS_LOCATION)'
libexecdir=${prefix}/libexec
AC_OUTPUT(
lsf.pm:lsf.in
)
If this script exits with a non-zero error code, then the setup script propagates the
error to the caller and exits without installing the service.
Registering as a Gatekeeper Service
Next, the setup script installs it's perl module into the perl library directory and
registers an entry in the Globus Gatekeeper's service directory. The program globus-job-
manager-service (distributed in the job manager program setup package) performs both of
these tasks. When run, it expects the scheduler perl module to be located in the
$GLOBUS_LOCATION/setup/globus directory.
$libexecdir/globus-job-manager-service -add -m lsf -s jobmanager-lsf;
Installing an RSL Validation File
If the scheduler script implements RSL attributes which are not part of the core set
supported by the job manager, it must publish them in the job manager's data directory. If
the scheduler script wants to set some default values of RSL attributes, it may also set
those as the default values in the validation file.
The format of the validation file is described in the RSL Validation File Format section
of the documentation. The validation file must be named scheduler-type.rvf and installed
in the $GLOBUS_LOCATION/share/globus_gram_job_manager directory.
In the LSF setup script, we check the list of queues supported by the local LSF
installation, and add a section of acceptable values for the queue RSL attribute:
open(VALIDATION_FILE,
">$ENV{GLOBUS_LOCATION}/share/globus_gram_job_manager/lsf.rvf");
# Customize validation file with queue info
open(BQUEUES, "bqueues -w |");
# discard header
$_ = <BQUEUES>;
my @queues = ();
while(<BQUEUES>)
{
chomp;
$_ =~ m/^()/;
push(@queues, $1);
}
close(BQUEUES);
if(@queues)
{
print VALIDATION_FILE "Attribute: queue0;
print VALIDATION_FILE join(" ", "Values:", @queues);
}
close VALIDATION_FILE;
Updating GPT Metadata
Finally, the setup package should create and finalize a Grid::GPT::Setup. The value of
$package must be the same value as the gpt_package_metadata Name attribute in the
package's metadata file. If either the new() or finish() methods fail, then it is
considered good practice to clean up any files created by the setup script. From setup-
globus-job-manager-lsf.pl:
my $metadata =
new Grid::GPT::Setup(
package_name => "globus_gram_job_manager_setup_lsf");
...
$metadata->finish();
Packaging
Now that we've written a job manager scheduler interface, we'll package it using GPT to
make it easy for our users to build and install. We'll start by gathering the different
files we've written above into a single directory lsf.
• lsf.in
• find-lsf-tools.in
• setup-globus-job-manager.pl
Package Documentation
If there are any scheduler-specific options defined for this scheduler module, or if there
any any optional setup items, then it is good to provide a documentation page which
describes these. For LSF, we describe the changes since the last version of this package
in the file globus_gram_job_manager_lsf.dox. This file consists of a doxygen mainpage. See
www.doxygen.org for information on how to write documentation with that tool.
configure.in
Now, we'll write our configure.in script. This file is converted to the configure shell
script by the bootstrap script below. Since we don't do any probes for compile-time tools
or system characteristics, we just call the various initialization macros used by GPT,
declare that we may provide doxygen documentation, and then output the files we need
substitions done on.
AC_REVISION($Revision: 1.7 $)
AC_INIT(Makefile.am)
GLOBUS_INIT
AM_PROG_LIBTOOL
dnl Initialize the automake rules the last argument
AM_INIT_AUTOMAKE($GPT_NAME, $GPT_VERSION)
LAC_DOXYGEN("../", "*.dox")
GLOBUS_FINALIZE
AC_OUTPUT(
Makefile
pkgdata/Makefile
pkgdata/pkg_data_src.gpt
doxygen/Doxyfile
doxygen/Doxyfile-internal
doxygen/Makefile
)
Package Metadata
Now we'll write our metadata file, and put it in the pkgdata subdirectory of our package.
The important things to note in this file are the package name and version, the
post_install_program, and the setup sections. These define how the package distribution
will be named, what command will be run by gpt-postinstall when this package is installed,
and what the setup dependencies will be written when the Grid::GPT::Setup object is
finalized.
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE gpt_package_metadata SYSTEM "package.dtd">
<gpt_package_metadata Format_Version="0.02" Name="globus_gram_job_manager_setup_lsf" >
<Aging_Version Age="0" Major="1" Minor="0" />
<Description >LSF Job Manager Setup</Description>
<Functional_Group >ResourceManagement</Functional_Group>
<Version_Stability Release="Beta" />
<src_pkg >
<With_Flavors build="no" />
<Source_Setup_Dependency PkgType="pgm" >
<Setup_Dependency Name="globus_gram_job_manager_setup" >
<Version >
<Simple_Version Major="3" />
</Version>
</Setup_Dependency>
</Source_Setup_Dependency>
<Build_Environment >
<cflags >@GPT_CFLAGS@</cflags>
<external_includes >@GPT_EXTERNAL_INCLUDES@</external_includes>
<pkg_libs > </pkg_libs>
<external_libs >@GPT_EXTERNAL_LIBS@</external_libs>
</Build_Environment>
<Post_Install_Message >
Run the setup-globus-job-manager-lsf setup script to configure an
lsf job manager.
</Post_Install_Message>
<Post_Install_Program >
setup-globus-job-manager-lsf
</Post_Install_Program>
<Setup Name="globus_gram_job_manager_service_setup" >
<Aging_Version Age="0" Major="1" Minor="0" />
</Setup>
</src_pkg>
</gpt_package_metadata>
Automake Makefile.am
The automake Makefile.am for this package is short because there isn't any compilation
needed for this package. We just need to define what needs to be installed into which
directory, and what source files need to be put inot our source distribution. For the LSF
package, we need to list the lsf.in, find-lsf-tools, and setup-globus-job-manager-lsf.pl
scripts as files to be installed into the setup directory. We need to add those files plus
our documentation source file to the EXTRA_LIST variable so that they will be included in
source distributions. The rest of the lines in the file are needed for proper interaction
with GPT.
include $(top_srcdir)/globus_automake_pre
include $(top_srcdir)/globus_automake_pre_top
SUBDIRS = pkgdata doxygen
setup_SCRIPTS = lsf.in find-lsf-tools setup-globus-job-manager-lsf.pl
EXTRA_DIST = $(setup_SCRIPTS) globus_gram_job_manager_lsf.dox
include $(top_srcdir)/globus_automake_post
include $(top_srcdir)/globus_automake_post_top
Bootstrap
The final piece we need to write for our package is the bootstrap script. This script is
the standard bootstrap script for a globus package, with an extra line to generate the
fine-lsf-tools script using autoconf.
#!/bin/sh
# checking for the GLOBUS_LOCATION
if test "x$GLOBUS_LOCATION" = "x"; then
echo "ERROR Please specify GLOBUS_LOCATION" >&2
exit 1
fi
if [ ! -f ${GLOBUS_LOCATION}/libexec/globus-bootstrap.sh ]; then
echo "ERROR: Unable to locate GLOBUS_LOCATION}/libexec/globus-bootstrap.sh"
echo " Please ensure that you have installed the globus-core package and"
echo " that GLOBUS_LOCATION is set to the proper directory"
exit
fi
. ${GLOBUS_LOCATION}/libexec/globus-bootstrap.sh
autoconf find-lsf-tools.in > find-lsf-tools
chmod 755 find-lsf-tools
exit 0
Building, Testing, and Debugging
With this all done, we can now try to build our now package. To do so, we'll need to run
% ./bootstrap
% ./globus-build
If all of the files are written correctly, this should result in our package being
installed into $GLOBUS_LOCATION. Once that is done, we should be able to run gpt-
postinstall to configure our new job manager.
Now, we should be able to run the command
% globus-personal-gatekeeper -start -jmtype lsf
to start a gatekeeper configured to run a job manager using our new scripts. Running this
will output a contact string (referred to as <contact-string> below), which we can use to
connect to this new service. To do so, we'll run globus-job-run to submit a test job:
% globus-job-run <contact-string> /bin/echo Hello, LSF
Hello, LSF
When Things Go Wrong
If the test above fails, or more complicated job failures are occurring, then you'lll have
to debug your scheduler interface. Here are a few tips to help you out.
Make sure that your script is valid Perl. If you run
perl -I$GLOBUS_LOCATION/lib/perl $GLOBUS_LOCATION/lib/perl/Globus/GRAM/JobManager/lsf.pm
You should get no output. If there are any diagnostics, correct them (in the lsf.in file),
reinstall your package, and rerun the setup script.
Look at the Globus Toolkit Error FAQ and see if the failure is perhaps not related to your
scheduler script at all.
Enable logging for the job manager. By default, the job manager is configured to log only
when it notices a job failure. However, if your problem is that your script is not
returning a failure code when you expect, you might want to enable logging always. To do
this, modify the job manager configuration file to contain '-save-logfile always' in
place of '-save-log on_error'.
Adding logging messages to your script: the JobManager object implements a log method,
which allows you to write messages to the job manager log file. Do this as your methods
are called to pinpoint where the error occurs.
Save the job description file when your script is run. This will allow you to run the
globus-job-manager-script.pl interactively (or in the Perl debugger). To save the job
description file, you can do
$self->{JobDescription}->save("/tmp/job_description.$$");
in any of the methods you've implemented.
Version 13.53 Sun Nov 24 globus_gram_job_manager_interface_tutorial(3)